How to delete a table in SQLAlchemy?

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Just call drop() against the table object.
From the docs:

Issue a DROP statement for this Table, using the given Connectable for connectivity.

In your case it should be:

User.__table__.drop()

If you get an exception like:

sqlalchemy.exc.UnboundExecutionError: Table object 'my_users' is not bound to an Engine or Connection. Execution can not proceed without a database to execute against

You need to pass the engine:

User.__table__.drop(engine)

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